Merged in zenodo (pull request #188)

zenodo json added
TheJacksonLaboratory · Apr 25, 2024 · 331bf8d · 331bf8d
2 parents dfa0451 + cc43d5f
commit 331bf8d
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Showing 4 changed files with 52 additions and 6 deletions.
diff --git a/.zenodo.json b/.zenodo.json
@@ -0,0 +1,46 @@
+{
+    "upload_type": "software", 
+    "description": "This is a GitHub action for releasing to Zenodo without giving webhook admin access",
+    "title": "Zenodo Release Action",
+    "creators": [
+        {
+            "affiliation": "The Jackson Laboratory",
+            "orcid": "0000-0003-1021-8129",
+            "name": "Michael Lloyd"
+        },
+        {
+            "affiliation": "The Jackson Laboratory",
+            "name": "Brian Sanderson"
+        },
+        {
+            "affiliation": "The Jackson Laboratory",
+            "name": "Barry Guglielmo"
+        },
+        {
+            "affiliation": "The Jackson Laboratory",
+            "name": "Sai Lek"
+        },
+        {
+            "affiliation": "The Jackson Laboratory",
+            "name": "Peter Fields"
+        },
+        {
+            "affiliation": "The Jackson Laboratory",
+            "name": "Harshpreet Chandok"
+        },
+        {
+            "affiliation": "The Jackson Laboratory",
+            "name": "Carolyn Paisie"
+        },
+        {
+            "affiliation": "The Jackson Laboratory",
+            "name": "Gabriel Rech"
+        },
+        {
+            "affiliation": "The Jackson Laboratory",
+            "name": "Anuj Srivastava"
+        }
+    ],
+    "keywords": ["zenodo", "release", "archive"],
+    "license": "MIT"
+  }
diff --git a/modules/r/annotate_genes_sv.nf b/modules/r/annotate_genes_sv.nf
@@ -2,8 +2,8 @@ process ANNOTATE_GENES_SV {
   tag "$sampleID"
 
   cpus 1
-  memory 8.GB
-  time '04:00:00'
+  memory 10.GB
+  time '10:00:00'
   errorStrategy {(task.exitStatus == 140) ? {log.info "\n\nError code: ${task.exitStatus} for task: ${task.name}. Likely caused by the task wall clock: ${task.time} or memory: ${task.memory} being exceeded.\nAttempting orderly shutdown.\nSee .command.log in: ${task.workDir} for more info.\n\n"; return 'finish'}.call() : 'finish'}
 
   container 'quay.io/jaxcompsci/r-sv_cnv_annotate:4.1.1'
@@ -17,7 +17,6 @@ process ANNOTATE_GENES_SV {
 
   script:
 
-
   if (suppl_switch == "main")
     """
     Rscript ${projectDir}/bin/pta/annotate-bedpe-with-genes.r \

diff --git a/modules/r/annotate_genes_sv_mouse.nf b/modules/r/annotate_genes_sv_mouse.nf
@@ -2,8 +2,8 @@ process ANNOTATE_GENES_SV {
   tag "$sampleID"
 
   cpus 1
-  memory 8.GB
-  time '04:00:00'
+  memory 10.GB
+  time '10:00:00'
   errorStrategy {(task.exitStatus == 140) ? {log.info "\n\nError code: ${task.exitStatus} for task: ${task.name}. Likely caused by the task wall clock: ${task.time} or memory: ${task.memory} being exceeded.\nAttempting orderly shutdown.\nSee .command.log in: ${task.workDir} for more info.\n\n"; return 'finish'}.call() : 'finish'}
 
   container 'quay.io/jaxcompsci/r-sv_cnv_annotate:4.1.1'
@@ -16,6 +16,7 @@ process ANNOTATE_GENES_SV {
     tuple val(sampleID), file("*.manta_lumpy_delly_svaba_sv_annotated_genes*.bed"), val(normal_name), val(tumor_name), emit: annot_sv_genes_bedpe
 
   script:    
+
   if (suppl_switch == "main")
     """
     Rscript ${projectDir}/bin/pta/annotate-bedpe-with-genes-mouse.r \

diff --git a/nextflow.config b/nextflow.config
@@ -45,7 +45,7 @@ manifest {
     homePage = "https://github.com/TheJacksonLaboratory/cs-nf-pipelines"
     mainScript = "main.nf"
     nextflowVersion = "!>=22.04.3"
-    version = "0.6.0"
+    version = "0.6.1"
     author = 'Michael Lloyd, Brian Sanderson, Barry Guglielmo, Sai Lek, Peter Fields, Harshpreet Chandok, Carolyn Paisie, Gabriel Rech, Anuj Srivastava. Copyright Jackson Laboratory 2024'
 }